Draft Genome Sequence of Lactobacillus johnsonii Strain 16, Isolated from Mice

Abstract

Here, we report the genome sequence of Lactobacillus johnsonii, a member of the gut lactobacilli. This draft genome of L. johnsonii strain 16 isolated from C57BL/6J mice enables the identification of bacterial genes responsible for host-specific gut persistence.

GENOME ANNOUNCEMENT

Lactobacillus johnsonii belongs to the lactic acid bacteria. It inhabits the gut of several hosts (1–6) and includes strains with probiotic activity (7–11). L. johnsonii levels were shown to be significantly higher in fecal samples of C57BL/6J mice than those of BALB/c. It was further suggested that the host genetics has a major effect on the persistence of L. johnsonii strain 16 in the gut of C57BL/6J mice (12). Here, we describe the draft genome sequence of L. johnsonii strain 16 isolated from a fecal sample of C57BL/6J mice in 2007, grown at Technion, Israel, and subjected to whole-genome shotgun sequencing.

Two different libraries, with average insert sizes of 330 bp and 3,700 bp, were prepared and sequenced using Illumina Genome Analyzer IIx, generating 5,908,676 31-bp paired-end reads and 4,615,910 31-bp mate-pair past-filtered reads, with a coverage of 183×. The reads of the two libraries were de novo assembled simultaneously with different insert lengths with Velvet 0.7.54 (13), generating 210 contigs of >100 bp using reads with a minimum quality of 30 for each base. The assembly covers 1,794,984 bp, with an N₅₀ of 34,798 bp and a longest segment of 118,507 bp. Mapping was done to validate the de novo assembly using MAQ 0.7.1 and BWA 0.5.8c (14), with a maximum of two differences from the reference sequence per read. Of the single reads, 95.6% were mapped to the assembly, and 80% of the single reads were mapped to the L. johnsonii NCC533 genome (15), covering 84.8% of the genome. In parallel, the 210 contigs were contiguated (aligned, ordered, and oriented), using ABACAS (16), to the L. johnsonii NCC 533 chromosome (15), which served as a reference genome. One scaffold that splits into 133 contigs was produced, with a total length of 1,491,125 bp, compared to 1,992,676 bp of the L. johnsonii NCC 533 genome. Seventy-seven contigs of the original 210 contigs could not be aligned to that reference genome. This implies that the human isolate L. johnsonii NCC 533 may not be a proper reference genome for the assembly of the mouse isolate L. johnsonii strain 16. Therefore, we relied on the de novo assembly, in which contigs <200 bp were removed.

The draft genome of L. johnsonii strain 16 consists of 156 segments covering 1.78 Mbp (34.6% G+C content). A total of 1,703 coding sequences (CDSs), 49 pseudogenes, 4 rRNAs, 42 tRNAs, and 1 noncoding RNA (ncRNA) were predicted and annotated by the NCBI Prokaryotic Genome Annotation Pipeline (17).

The whole-genome sequence of L. johnsonii strain 16 might lead to the discovery of bacterial genes that may be involved in bacterial persistence in the gut. In a previous study, we showed a phylogenetic separation among L. johnsonii isolates associated with the taxonomic classification of their hosts, indicating coevolution of the host and its gut bacteria (18). Thus, the gathered information on both host and bacterial genes involved in bacterial gut persistence call for the development of probiotic products specifically oriented to the consumer’s genetics as part of a personalized medicine approach.

Nucleotide sequence accession numbers.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under the accession no. LIGY00000000. The version described in this paper is version LIGY00000000.1.